[gmx-users] Harmonic restraint in FEP

[Alexander Alexander]

Dear Gromacs user,

To avoid conformational changes of a single amino acid while it is
perturbed (vdW and q --> 0) in Free energy calculation, I need to apply a
harmonic restraints on(or between?) some of it's atoms by [
distance_restraints ] and "restraint-lambdas".

First of all, is this right? I means " "restraint-lambdas" can be used for [
distance_restraints ]?

If so, how can I find out proper "low, up1, up2 and fac" for a molecule?

One more question is that what the "restraint-lambdas" should be look like
when harmonic restraints is going to be applied(turning on gradually) by
whatever method?


restraint-lambdas   = 1.0 0.8 0.6 0.4 0.2 0.0
OR
restraint-lambdas   = 0.0 0.2 0.4 0.6 0.8 1.0

Thanks in advance.
Regards,
Alex